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J Phys Chem B. 2015 Sep 24;119(38):12355-64. doi: 10.1021/acs.jpcb.5b05190. Epub 2015 Sep 14.

Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions.

Author information

1
Department of Medicinal Chemistry, College of Pharmacy, University of Utah , Salt Lake City, Utah 84112, United States.
2
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States.

Abstract

The Varkud Satellite RNA contains a self-cleaving ribozyme that has been shown to function independently of its surroundings. This 160 nucleotide ribozyme adopts a catalytically active tertiary structure that includes a kissing hairpin complex formed by stem-loop I and stem-loop V (SLV). The five-nucleotide 5'-rUGACU loop of the isolated SLV has been shown to adopt a Mg(2+)-dependent U-turn structure by solution NMR. This U-turn hairpin is examined here by molecular dynamics simulations in the presence of monovalent and divalent ions. Simulations confirm on an all-atom level the hypotheses for the role of the Mg(2+) ions in stabilizing the loop, as well as the role of the solvent exposed U700 base. Additionally, these simulations suggest the Mg(2+)-free stem-loop adopts a wide range of structures, including energetically favorable structures similar to the Mg(2+)-bound loop structure. We propose this structure is a "gatekeeper" or precursor to Mg(2+) binding when those ions are present.

PMID:
26328924
PMCID:
PMC4634716
DOI:
10.1021/acs.jpcb.5b05190
[Indexed for MEDLINE]
Free PMC Article

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